1. Login to `transit.uppmax.uu.se`
Documentation:
- https://uppmax.github.io/UPPMAX-documentation/cluster_guides/transfer_bianca/#transit-server
2. Mount the `wharf` of your project.

    user@transit:~$ mount_wharf sens2023531
    Mounting wharf (accessible for you only) to /home/<user>/sens2023531
    <user>[e-mail]'s password: 

4. Navigate to your `wharf` folder
5. Disable Singularity cache

   export SINGULARITY_DISABLE_CACHE=true
   export APPTAINER_DISABLE_CACHE=true
   unset NXF_SINGULARITY_CACHEDIR

5. Load nf-core software module

   module load uppmax bioinfo-tools nf-core/latest Nextflow/latest

7. Run `nf-core` to download the pipeline.

   nf-core download pixelator
                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.11.1 - https://nf-co.re

    WARNING  Could not find GitHub authentication token. Some API requests may fail.                                                    
    ? Select release / branch: 1.0.2  [release]
    ? Include the nf-core's default institutional configuration files into the download? Yes

    In addition to the pipeline code, this tool can download software containers.
    ? Download software container images: singularity

    Nextflow and nf-core can use an environment variable called $NXF_SINGULARITY_CACHEDIR that is a path to a directory where remote 
    Singularity images are stored. This allows downloaded images to be cached in a central location.
    ? Define $NXF_SINGULARITY_CACHEDIR for a shared Singularity image download folder? [y/n]: n

    If transferring the downloaded files to another system, it can be convenient to have everything compressed in a single file.
    This is not recommended when downloading Singularity images, as it can take a long time and saves very little space.
    ? Choose compression type: none
    INFO     Saving 'nf-core/pixelator'                                                                                                 
              Pipeline revision: '1.0.2'                                                                                                
              Use containers: 'singularity'                                                                                             
              Container library: 'quay.io'                                                                                              
              Output directory: 'nf-core-pixelator_1.0.2'                                                                               
              Include default institutional configuration: 'True'                                                                       
    INFO     Downloading centralised configs from GitHub                                                                                
    INFO     Downloading workflow files from GitHub                                                                                     
    INFO     Processing workflow revision 1.0.2, found 4 container images in     total.
    Downloading singularity images ???????????????????????????????????????????????????????????????????????????????? 100% ? 4/4 completed

8. Running on Bianca

    module load bioinfo-tools Nextflow
    nextflow run ... -profile uppmax --project sens-XXXX-XX .... 

Note: you might need `-c configs/conf/uppmax.config`, make sure you have the file (it is an option to download it during the pipeline download process).
https://github.com/nf-core/configs/blob/master/conf/uppmax.config
https://nf-co.re/configs/uppmax

## Contacts:
- [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425)
- [UPPMAX](https://www.uppmax.uu.se/)
- [AE@UPPMAX - related documentation](/8sqXISVRRquPDSw9o1DizQ)


###### tags: `UPPMAX`